MolNFT v1 · #137733 · protein

2.55 a resolution structure of ipad from shigella flexneri in complex with single-domain antibody jmk-H2

5VXK: “2.55 a resolution structure of ipad from shigella flexneri in complex with single-domain antibody jmk-H2”. X-ray diffraction, 1 pocket (best druggability 0.46). MolNFT v1 #137733 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5VXK
Type: protein
Length: 407 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-domain antibody jmk-H2; Invasin ipad
UniProt: P18013
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Single-domain antibody jmk-H2	protein	125	7% helix, 45% strand	—
A	Invasin ipad	protein	282	70% helix, 9% strand	P18013

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.46	0.75	22	empty

Interfaces

1 interface between chains.

B–A · 735 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5VXK · 2.55 A resolution structure of IpaD from Shigella flexneri in complex with single-domain… · the same entry in another collection · chain B against B, TM-score 1.00
P18013 · AlphaFold monomer V2.0 prediction for invasin ipad (P18013) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P18013
Elsewhere: RCSB PDB 5VXK · PDBe 5VXK · UniProt P18013

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